Hello,
I am looking to measure the diffusion coefficient of a subset of water
molecules moving through a pore in a lipid bilayer. In looking at g_msd and
the -mol option, the manual states that my index file needs references to
molecule numbers rather than atom numbers. I was wondering how I go about
this. The help for make_ndx is a bit unclear to me. It seems the selections
that I make all end up giving a reference to the atom number. Am I missing
something here? How do I get an index file with a reference to the molecule
number?
Thanks,
Mike Tomasini
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